Silicone is pretty resilient. A quality silicone is durable, can withstand high temperatures, is antimicrobial, and non porous. Pinching, poking, and scratching it shouldn’t cause any tears or cuts. I can’t say the same for your skin and delicate tissues, so tuck you nails inward while inserting your fingers.
However, there are some lesser quality cups on the market that are made so thin that it is possible for a nail to leave a mark. So it really depends on which cup you have.
I have long natrual nails. If I stretch my nail into the silicone on a reputable cup, the nail mark goes away within a few seconds if there’s a mark at all. On a lot of “cheapie” cups, if I do the same thing, sometimes the mark doesn’t go away. I have one cup that I did this two a couple of years ago and the mark is still there.
*More on quality silicone: Medical Grade Silicone vs “Cheapies”